
<!DOCTYPE html>

<html xmlns="http://www.w3.org/1999/xhtml">
  <head>
    <meta charset="utf-8" />
    <title>Dislocation &#8212; atomman 1.4.0 documentation</title>
    <link rel="stylesheet" href="_static/basic.css" type="text/css" />
    <link rel="stylesheet" href="_static/pygments.css" type="text/css" />
    <script type="text/javascript" id="documentation_options" data-url_root="./" src="_static/documentation_options.js"></script>
    <script type="text/javascript" src="_static/jquery.js"></script>
    <script type="text/javascript" src="_static/underscore.js"></script>
    <script type="text/javascript" src="_static/doctools.js"></script>
    <script type="text/javascript" src="_static/language_data.js"></script>
    <script crossorigin="anonymous" integrity="sha256-Ae2Vz/4ePdIu6ZyI/5ZGsYnb+m0JlOmKPjt6XZ9JJkA=" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.4/require.min.js"></script>
    <script async="async" type="text/javascript" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/latest.js?config=TeX-AMS-MML_HTMLorMML"></script>
    <script type="text/x-mathjax-config">MathJax.Hub.Config({"tex2jax": {"inlineMath": [["$", "$"], ["\\(", "\\)"]], "processEscapes": true, "ignoreClass": "document", "processClass": "math|output_area"}})</script>
    <link rel="index" title="Index" href="genindex.html" />
    <link rel="search" title="Search" href="search.html" />
    <link rel="next" title="DifferentialDisplacement" href="atomman.defect.DifferentialDisplacement.html" />
    <link rel="prev" title="Stroh" href="atomman.defect.Stroh.html" /> 
  </head><body>
    <div class="related" role="navigation" aria-label="related navigation">
      <h3>Navigation</h3>
      <ul>
        <li class="right" style="margin-right: 10px">
          <a href="genindex.html" title="General Index"
             accesskey="I">index</a></li>
        <li class="right" >
          <a href="py-modindex.html" title="Python Module Index"
             >modules</a> |</li>
        <li class="right" >
          <a href="atomman.defect.DifferentialDisplacement.html" title="DifferentialDisplacement"
             accesskey="N">next</a> |</li>
        <li class="right" >
          <a href="atomman.defect.Stroh.html" title="Stroh"
             accesskey="P">previous</a> |</li>
        <li class="nav-item nav-item-0"><a href="index.html">atomman 1.4.0 documentation</a> &#187;</li>
          <li class="nav-item nav-item-1"><a href="atomman.html" >atomman package</a> &#187;</li>
          <li class="nav-item nav-item-2"><a href="atomman.defect.html" accesskey="U">defect</a> &#187;</li> 
      </ul>
    </div>  

    <div class="document">
      <div class="documentwrapper">
        <div class="bodywrapper">
          <div class="body" role="main">
            
  <div class="section" id="dislocation">
<h1>Dislocation<a class="headerlink" href="#dislocation" title="Permalink to this headline">¶</a></h1>
<dl class="class">
<dt id="atomman.defect.Dislocation">
<em class="property">class </em><code class="sig-prename descclassname">atomman.defect.</code><code class="sig-name descname">Dislocation</code><span class="sig-paren">(</span><em class="sig-param">ucell, C, burgers, ξ_uvw, slip_hkl, m=[0, 1, 0], n=[0, 0, 1], shift=None, shiftindex=None, shiftscale=None, tol=1e-08</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.defect.Dislocation" title="Permalink to this definition">¶</a></dt>
<dd><p>Bases: <a class="reference external" href="https://docs.python.org/3/library/functions.html#object" title="(in Python v3.9)"><code class="xref py py-class docutils literal notranslate"><span class="pre">object</span></code></a></p>
<dl class="method">
<dt id="atomman.defect.Dislocation.array_boundary">
<code class="sig-name descname">array_boundary</code><span class="sig-paren">(</span><em class="sig-param">box</em>, <em class="sig-param">width</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.defect.Dislocation.array_boundary" title="Permalink to this definition">¶</a></dt>
<dd><p>Constructs a shape associated with the boundary regions used by the
periodicarray() generation method.  The returned shape will encompass
all atoms except those within width distance of the non-periodic
surface.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>box</strong> (<a class="reference internal" href="atomman.Box.html#atomman.Box" title="atomman.Box"><em>atomman.Box</em></a>) – The box associated with the full (base) system.</p></li>
<li><p><strong>width</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a>) – The width of the boundary region</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The Shape object excluding the boundary region</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference internal" href="atomman.region.html#atomman.region.PlaneSet" title="atomman.region.PlaneSet">atomman.region.PlaneSet</a></p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.Dislocation.base_system">
<em class="property">property </em><code class="sig-name descname">base_system</code><a class="headerlink" href="#atomman.defect.Dislocation.base_system" title="Permalink to this definition">¶</a></dt>
<dd><p>The “perfect crystal” reference system associated with the dislocation system</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p><a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System">atomman.System</a></p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.Dislocation.box_boundary">
<code class="sig-name descname">box_boundary</code><span class="sig-paren">(</span><em class="sig-param">box</em>, <em class="sig-param">width</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.defect.Dislocation.box_boundary" title="Permalink to this definition">¶</a></dt>
<dd><p>Constructs a shape associated with the box-style boundary region.  Used
by the monopole() generation method.  The returned shape will encompass
all atoms except those within width distance of the two non-periodic
surfaces.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>box</strong> (<a class="reference internal" href="atomman.Box.html#atomman.Box" title="atomman.Box"><em>atomman.Box</em></a>) – The box associated with the full (base) system.</p></li>
<li><p><strong>width</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a>) – The width of the boundary region</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The Shape object excluding the boundary region</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference internal" href="atomman.region.html#atomman.region.PlaneSet" title="atomman.region.PlaneSet">atomman.region.PlaneSet</a></p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.Dislocation.cutindex">
<em class="property">property </em><code class="sig-name descname">cutindex</code><a class="headerlink" href="#atomman.defect.Dislocation.cutindex" title="Permalink to this definition">¶</a></dt>
<dd><p>0=a, 1=b, 2=c</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.9)">int</a></p>
</dd>
<dt class="field-even">Type</dt>
<dd class="field-even"><p>The index of the box vector that is not within the slip plane</p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.Dislocation.cylinder_boundary">
<code class="sig-name descname">cylinder_boundary</code><span class="sig-paren">(</span><em class="sig-param">box</em>, <em class="sig-param">width</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.defect.Dislocation.cylinder_boundary" title="Permalink to this definition">¶</a></dt>
<dd><p>Constructs a shape associated with the cylinder-style boundary region.
Used by the monopole() generation method.  The returned shape will
encompass a cylinder of atoms centered around the dislocation line
leaving a boundary region that will be at least width wide everywhere.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>box</strong> (<a class="reference internal" href="atomman.Box.html#atomman.Box" title="atomman.Box"><em>atomman.Box</em></a>) – The box associated with the full (base) system.</p></li>
<li><p><strong>width</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a>) – The minimum width of the boundary region.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p>The Shape object excluding the boundary region</p>
</dd>
<dt class="field-odd">Return type</dt>
<dd class="field-odd"><p><a class="reference internal" href="atomman.region.html#atomman.region.Cylinder" title="atomman.region.Cylinder">atomman.region.Cylinder</a></p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.Dislocation.disl_system">
<em class="property">property </em><code class="sig-name descname">disl_system</code><a class="headerlink" href="#atomman.defect.Dislocation.disl_system" title="Permalink to this definition">¶</a></dt>
<dd><p>The generated dislocation system</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p><a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System">atomman.System</a></p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.Dislocation.dislsol">
<em class="property">property </em><code class="sig-name descname">dislsol</code><a class="headerlink" href="#atomman.defect.Dislocation.dislsol" title="Permalink to this definition">¶</a></dt>
<dd><p>The elastic dislocation solution</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p><a class="reference internal" href="atomman.defect.VolterraDislocation.html#atomman.defect.VolterraDislocation" title="atomman.defect.VolterraDislocation">atomman.defect.VolterraDislocation</a></p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.Dislocation.fromref">
<em class="property">classmethod </em><code class="sig-name descname">fromref</code><span class="sig-paren">(</span><em class="sig-param">ucell</em>, <em class="sig-param">C</em>, <em class="sig-param">model</em>, <em class="sig-param">tol=1e-08</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.defect.Dislocation.fromref" title="Permalink to this definition">¶</a></dt>
<dd><p>Initializes a Dislocation object based on pre-defined dislocation
parameters from a reference record.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>ucell</strong> (<a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System"><em>atomman.System</em></a>) – The unit cell to use as the seed for generating the dislocation
monopole system.</p></li>
<li><p><strong>C</strong> (<a class="reference internal" href="atomman.ElasticConstants.html#atomman.ElasticConstants" title="atomman.ElasticConstants"><em>atomman.ElasticConstants</em></a>) – The elastic constants associated with the bulk crystal structure
for ucell.</p></li>
<li><p><strong>model</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>file-like object</em><em> or </em><em>DataModelDict</em>) – The reference record containing dislocation parameters to use.</p></li>
<li><p><strong>tol</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a>) – A cutoff tolerance used with obtaining the dislocation solution.
Only needs to be changed if there are issues with obtaining a
solution.</p></li>
</ul>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.Dislocation.lineindex">
<em class="property">property </em><code class="sig-name descname">lineindex</code><a class="headerlink" href="#atomman.defect.Dislocation.lineindex" title="Permalink to this definition">¶</a></dt>
<dd><p>0=a, 1=b, 2=c</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/functions.html#int" title="(in Python v3.9)">int</a></p>
</dd>
<dt class="field-even">Type</dt>
<dd class="field-even"><p>The index of the box vector that coincides with the dislocation line</p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.Dislocation.monopole">
<code class="sig-name descname">monopole</code><span class="sig-paren">(</span><em class="sig-param">sizemults=None</em>, <em class="sig-param">amin=0.0</em>, <em class="sig-param">bmin=0.0</em>, <em class="sig-param">cmin=0.0</em>, <em class="sig-param">shift=None</em>, <em class="sig-param">shiftindex=None</em>, <em class="sig-param">shiftscale=False</em>, <em class="sig-param">boundaryshape='cylinder'</em>, <em class="sig-param">boundarywidth=0.0</em>, <em class="sig-param">boundaryscale=False</em>, <em class="sig-param">return_base_system=False</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.defect.Dislocation.monopole" title="Permalink to this definition">¶</a></dt>
<dd><p>Constructs a dislocation monopole atomic configuration containing a
single perfectly straight dislocation. The resulting system will be
periodic along the box vector direction that corresponds to the
dislocation’s line direction, and non-periodic in the other two box
vector directions.  Boundary atoms near the two free surfaces will be
identified by changing their atype values making it easy to identify
them later for assigning different boundary conditions.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>sizemults</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.9)"><em>tuple</em></a><em>, </em><em>optional</em>) – The size multipliers to use when generating the system.  Values are
limited to being positive integers.  The multipliers for the two
non-periodic directions must be even.  If not given, the default
multipliers will be 2 for the non-periodic directions and 1 for the
periodic direction.</p></li>
<li><p><strong>amin</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – A minimum thickness to use for the a box vector direction of the
final system.  Default value is 0.0.  For the non-periodic
directions, the resulting vector multiplier will be even.  If both
amin and sizemults is given, then the larger multiplier for the two
will be used.</p></li>
<li><p><strong>bmin</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – A minimum thickness to use for the b box vector direction of the
final system.  Default value is 0.0.  For the non-periodic
directions, the resulting vector multiplier will be even.  If both
bmin and sizemults is given, then the larger multiplier for the two
will be used.</p></li>
<li><p><strong>cmin</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – A minimum thickness to use for the c box vector direction of the
final system.  Default value is 0.0.  For the non-periodic
directions, the resulting vector multiplier will be even.  If both
cmin and sizemults is given, then the larger multiplier for the two
will be used.</p></li>
<li><p><strong>shift</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – A rigid body shift to apply to the rotated cell prior to inserting
the dislocation.  Should be selected such that the ideal slip plane
does not correspond to any atomic planes.  Is taken as absolute if
shiftscale is False, or relative to the rotated cell’s box vectors
if shiftscale is True.  Cannot be given with shiftindex.  If
neither shift nor shiftindex is given will use the shift set during
class initialization.</p></li>
<li><p><strong>shiftindex</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – The index of the identified optimum shifts based on the rotated
cell to use.  Different values allow for the selection of different
atomic planes neighboring the slip plane.  Note that shiftindex
values only apply shifts normal to the slip plane; best shifts for
non-planar dislocations (like bcc screw) may also need a shift in
the slip plane.  Cannot be given with shiftindex.  If neither shift
nor shiftindex is given then shiftindex = 0 is used then will use
the shift set during class initialization.</p></li>
<li><p><strong>shiftscale</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – If False (default), a given shift value will be taken as absolute
Cartesian.  If True, a given shift will be taken relative to the
rotated cell’s box vectors.</p></li>
<li><p><strong>boundaryshape</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#str" title="(in Python v3.9)"><em>str</em></a><em>, </em><em>optional</em>) – Indicates the shape of the boundary region to use.  Options are
‘cylinder’ (default) and ‘box’.  For ‘cylinder’, the non-boundary
region is defined by a cylinder with axis along the dislocation
line and a radius that ensures the boundary is at least
boundarywidth thick.  For ‘box’, the boundary region will be
exactly boundarywidth thick all around.</p></li>
<li><p><strong>boundarywidth</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – The width of the boundary region to apply.  Default value is 0.0,
i.e. no boundary region.  All atoms in the boundary region will
have their atype values changed.</p></li>
<li><p><strong>boundaryscale</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – If False (Default), the boundarywidth will be taken as absolute.
If True, the boundarywidth will be taken relative to the magnitude
of the unit cell’s a box vector.</p></li>
<li><p><strong>return_base_system</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – If True then the dislocation-free base system corresponding to the
dislocation system will also be returned.  The base system is used
as a reference state for most of the dislocation analysis tools.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><ul class="simple">
<li><p><strong>base_system</strong> (<em>atomman.System</em>) – The base “perfect crystal” reference system associated with the
dislocation system. Only returned if return_base_system is True.</p></li>
<li><p><strong>disl_system</strong> (<em>atomman.System</em>) – The generated dislocation monopole system.</p></li>
</ul>
</p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.Dislocation.periodicarray">
<code class="sig-name descname">periodicarray</code><span class="sig-paren">(</span><em class="sig-param">sizemults=None</em>, <em class="sig-param">amin=0.0</em>, <em class="sig-param">bmin=0.0</em>, <em class="sig-param">cmin=0.0</em>, <em class="sig-param">shift=None</em>, <em class="sig-param">shiftindex=None</em>, <em class="sig-param">shiftscale=False</em>, <em class="sig-param">boundarywidth=0.0</em>, <em class="sig-param">boundaryscale=False</em>, <em class="sig-param">linear=False</em>, <em class="sig-param">cutoff=None</em>, <em class="sig-param">return_base_system=False</em><span class="sig-paren">)</span><a class="headerlink" href="#atomman.defect.Dislocation.periodicarray" title="Permalink to this definition">¶</a></dt>
<dd><p>Constructs a dislocation monopole atomic configuration containing a
single perfectly straight dislocation. The resulting system will be
periodic along the box vector direction that corresponds to the
dislocation’s line direction, and non-periodic in the other two box
vector directions.  Boundary atoms near the two free surfaces will be
identified by changing their atype values making it easy to identify
them later for assigning different boundary conditions.</p>
<dl class="field-list simple">
<dt class="field-odd">Parameters</dt>
<dd class="field-odd"><ul class="simple">
<li><p><strong>sizemults</strong> (<a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#tuple" title="(in Python v3.9)"><em>tuple</em></a><em>, </em><em>optional</em>) – The size multipliers to use when generating the system.  Values
are limited to being positive integers.  The multipliers for the
two non-periodic directions must be even.  If not given, the
default multipliers will be 2 for the non-periodic directions and
1 for the periodic direction.</p></li>
<li><p><strong>amin</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – A minimum thickness to use for the a box vector direction of the
final system.  Default value is 0.0.  For the non-periodic
directions, the resulting vector multiplier will be even.  If both
amin and sizemults is given, then the larger multiplier for the two
will be used.</p></li>
<li><p><strong>bmin</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – A minimum thickness to use for the b box vector direction of the
final system.  Default value is 0.0.  For the non-periodic
directions, the resulting vector multiplier will be even.  If both
bmin and sizemults is given, then the larger multiplier for the two
will be used.</p></li>
<li><p><strong>cmin</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – A minimum thickness to use for the c box vector direction of the
final system.  Default value is 0.0.  For the non-periodic
directions, the resulting vector multiplier will be even.  If both
cmin and sizemults is given, then the larger multiplier for the two
will be used.</p></li>
<li><p><strong>shift</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – A rigid body shift to apply to the rotated cell prior to inserting
the dislocation.  Should be selected such that the ideal slip plane
does not correspond to any atomic planes.  Is taken as absolute if
shiftscale is False, or relative to the rotated cell’s box vectors
if shiftscale is True.  Cannot be given with shiftindex.  If
neither shift nor shiftindex is given then shiftindex = 0 is used.</p></li>
<li><p><strong>shiftindex</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – The index of the identified optimum shifts based on the rotated
cell to use.  Different values allow for the selection of different
atomic planes neighboring the slip plane.  Note that shiftindex
values only apply shifts normal to the slip plane; best shifts for
non-planar dislocations (like bcc screw) may also need a shift in
the slip plane.  Cannot be given with shiftindex.  If neither shift
nor shiftindex is given then shiftindex = 0 is used.</p></li>
<li><p><strong>shiftscale</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – If False (default), a given shift value will be taken as absolute
Cartesian.  If True, a given shift will be taken relative to the
rotated cell’s box vectors.</p></li>
<li><p><strong>boundarywidth</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – The width of the boundary region to apply.  Default value is 0.0,
i.e. no boundary region.  All atoms in the boundary region will
have their atype values changed and will be displaced by linear
displacements.</p></li>
<li><p><strong>boundaryscale</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – If False (Default), the boundarywidth will be taken as absolute.
If True, the boundarywidth will be taken relative to the magnitude
of the unit cell’s a box vector.</p></li>
<li><p><strong>linear</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – If True, then only linear displacements will be used and not the
dislocation solution.  Using only linear displacements is useful
for screw dislocations and dislocations with large stacking fault
distances.  If False (default) then the dislocation solution will
be used for the middle displacements and linear displacements only
in the boundary region.</p></li>
<li><p><strong>cutoff</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#float" title="(in Python v3.9)"><em>float</em></a><em>, </em><em>optional</em>) – Cutoff distance to use for identifying duplicate atoms to remove.
For dislocations with an edge component, applying the displacements
creates an extra half-plane of atoms that will have (nearly)
identical positions with other atoms after altering the boundary
conditions.  Default value is 0.5 Angstrom.</p></li>
<li><p><strong>return_base_system</strong> (<a class="reference external" href="https://docs.python.org/3/library/functions.html#bool" title="(in Python v3.9)"><em>bool</em></a><em>, </em><em>optional</em>) – If True then the dislocation-free base system corresponding to the
dislocation system will also be returned.  The base system is used
as a reference state for most of the dislocation analysis tools.</p></li>
</ul>
</dd>
<dt class="field-even">Returns</dt>
<dd class="field-even"><p><ul class="simple">
<li><p><strong>base_system</strong> (<em>atomman.System</em>) – The base “perfect crystal” reference system associated with the
dislocation system.  If the Burgers vector has an edge component
then the atoms deleted when generating disl_system will also be
deleted from base_system. Only returned if return_base_system is
True.</p></li>
<li><p><strong>disl_system</strong> (<em>atomman.System</em>) – The generated periodic array of dislocations system.</p></li>
</ul>
</p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.Dislocation.rcell">
<em class="property">property </em><code class="sig-name descname">rcell</code><a class="headerlink" href="#atomman.defect.Dislocation.rcell" title="Permalink to this definition">¶</a></dt>
<dd><p>The cell associated with rotating ucell to coincide with the dislocation solution</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p><a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System">atomman.System</a></p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.Dislocation.shift">
<em class="property">property </em><code class="sig-name descname">shift</code><a class="headerlink" href="#atomman.defect.Dislocation.shift" title="Permalink to this definition">¶</a></dt>
<dd><p>The particular shift value that will be or was used to construct the dislocation system</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p>numpy.NDArray</p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.Dislocation.shifts">
<em class="property">property </em><code class="sig-name descname">shifts</code><a class="headerlink" href="#atomman.defect.Dislocation.shifts" title="Permalink to this definition">¶</a></dt>
<dd><p>All identified shifts that will place the slip plane halfway between atomic planes</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p><a class="reference external" href="https://docs.python.org/3/library/stdtypes.html#list" title="(in Python v3.9)">list</a></p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.Dislocation.transform">
<em class="property">property </em><code class="sig-name descname">transform</code><a class="headerlink" href="#atomman.defect.Dislocation.transform" title="Permalink to this definition">¶</a></dt>
<dd><p>The 3x3 Cartesian transformation matrix associated with rotating from ucell to rcell</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p>numpy.NDArray</p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.Dislocation.ucell">
<em class="property">property </em><code class="sig-name descname">ucell</code><a class="headerlink" href="#atomman.defect.Dislocation.ucell" title="Permalink to this definition">¶</a></dt>
<dd><p>The crystal unit cell used as the basis for constructing the dislocation system</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p><a class="reference internal" href="atomman.System.html#atomman.System" title="atomman.System">atomman.System</a></p>
</dd>
</dl>
</dd></dl>

<dl class="method">
<dt id="atomman.defect.Dislocation.uvws">
<em class="property">property </em><code class="sig-name descname">uvws</code><a class="headerlink" href="#atomman.defect.Dislocation.uvws" title="Permalink to this definition">¶</a></dt>
<dd><p>The 3x3 array of uvw Miller vectors used to rotate ucell to rcell</p>
<dl class="field-list simple">
<dt class="field-odd">Type</dt>
<dd class="field-odd"><p>numpy.NDArray</p>
</dd>
</dl>
</dd></dl>

</dd></dl>

</div>


          </div>
        </div>
      </div>
      <div class="sphinxsidebar" role="navigation" aria-label="main navigation">
        <div class="sphinxsidebarwrapper">
  <h4>Previous topic</h4>
  <p class="topless"><a href="atomman.defect.Stroh.html"
                        title="previous chapter">Stroh</a></p>
  <h4>Next topic</h4>
  <p class="topless"><a href="atomman.defect.DifferentialDisplacement.html"
                        title="next chapter">DifferentialDisplacement</a></p>
        </div>
      </div>
      <div class="clearer"></div>
    </div>
    <div class="related" role="navigation" aria-label="related navigation">
      <h3>Navigation</h3>
      <ul>
        <li class="right" style="margin-right: 10px">
          <a href="genindex.html" title="General Index"
             >index</a></li>
        <li class="right" >
          <a href="py-modindex.html" title="Python Module Index"
             >modules</a> |</li>
        <li class="right" >
          <a href="atomman.defect.DifferentialDisplacement.html" title="DifferentialDisplacement"
             >next</a> |</li>
        <li class="right" >
          <a href="atomman.defect.Stroh.html" title="Stroh"
             >previous</a> |</li>
        <li class="nav-item nav-item-0"><a href="index.html">atomman 1.4.0 documentation</a> &#187;</li>
          <li class="nav-item nav-item-1"><a href="atomman.html" >atomman package</a> &#187;</li>
          <li class="nav-item nav-item-2"><a href="atomman.defect.html" >defect</a> &#187;</li> 
      </ul>
    </div>
    <div class="footer" role="contentinfo">
      Created using <a href="http://sphinx-doc.org/">Sphinx</a> 2.2.0.
    </div>
  </body>
</html>